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From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome

Published online by Cambridge University Press:  14 December 2011

Maria W. Górna ,
Agamemnon J. Carpousis  and
Ben F. Luisi
Maria W. Górna
Affiliation:
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
Agamemnon J. Carpousis
Affiliation:
Laboratoire de Microbiologie et Génétique Moléculaires, CNRS et Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
Ben F. Luisi*
Affiliation:
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
*
*Author for correspondence: Ben F. Luisi, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Email: bfl20@mole.bio.cam.ac.uk.
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Abstract

The RNA degradosome is a massive multi-enzyme assembly that occupies a nexus in RNA metabolism and post-transcriptional control of gene expression in Escherichia coli and many other bacteria. Powering RNA turnover and quality control, the degradosome serves also as a machine for processing structured RNA precursors during their maturation. The capacity to switch between destructive and processing modes involves cooperation between degradosome components and is analogous to the process of RNA surveillance in other domains of life. Recruitment of components and cellular compartmentalisation of the degradosome are mediated through small recognition domains that punctuate a natively unstructured segment within a scaffolding core. Dynamic in conformation, variable in composition and non-essential under certain laboratory conditions, the degradosome has nonetheless been maintained throughout the evolution of many bacterial species, due most likely to its diverse contributions in global cellular regulation. We describe the role of the degradosome and its components in RNA decay pathways in E. coli, and we broadly compare these pathways in other bacteria as well as archaea and eukaryotes. We discuss the modular architecture and molecular evolution of the degradosome, its roles in RNA degradation, processing and quality control surveillance, and how its activity is regulated by non-coding RNA. Parallels are drawn with analogous machinery in organisms from all life domains. Finally, we conjecture on roles of the degradosome as a regulatory hub for complex cellular processes.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 45 , Issue 2 , May 2012 , pp. 105 - 145
Copyright
Copyright © Cambridge University Press 2011

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References

7. References

Afonyushkin, T., Vecerek, B., Moll, I., Bläsi, U. & Kaberdin, V. R. (2005). Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Research 33, 1678–1689.CrossRefGoogle ScholarPubMed
Ait-Bara, S. & Carpousis, A. J. (2010). Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E–RhlB interaction in the gammaproteobacteria. Journal of Bacteriology 192, 5413–5423.CrossRefGoogle ScholarPubMed
Anantharaman, V., Koonin, E. V. & Aravind, L. (2002). Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Research 30, 1427–1464.CrossRefGoogle ScholarPubMed
Andrade, J. M. & Arraiano, C. M. (2008). PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA 14, 543–551.CrossRefGoogle ScholarPubMed
Andrade, J. M., Pobre, V., Silva, I. J., Domingues, S. & Arraiano, C. M. (2009). The role of 3′–5′ exoribonucleases in RNA degradation. Progress in Molecular Biology and Translational Science 85, 187–229.CrossRefGoogle ScholarPubMed
Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E. G., Margalit, H. & Altuvia, S. (2001). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology 11, 941–950.CrossRefGoogle ScholarPubMed
Arnold, T. E., Yu, J. & Belasco, J. G. (1998). mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4, 319–330.Google ScholarPubMed
Babitzke, P. & Romeo, T. (2007). CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Current Opinion in Microbiology 10, 156–163.CrossRefGoogle ScholarPubMed
Barak, I., Muchova, K., Wilkinson, A. J., O'Toole, P. J. & Pavlendova, N. (2008). Lipid spirals in Bacillus subtilis and their role in cell division. Molecular Microbiology 68, 1315–1327.CrossRefGoogle ScholarPubMed
Basturea, G. N., Zundel, M. A. & Deutscher, M. P. (2011). Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH. RNA 17, 338–345.CrossRefGoogle Scholar
Beich-Frandsen, M., Vecerek, B., Konarev, P. V., Sjoblom, B., Kloiber, K., Hammerle, H., Rajkowitsch, L., Miles, A. J., Kontaxis, G., Wallace, B. A., Svergun, D. I., Konrat, R., Blasi, U. & Djinovic-Carugo, K. (2011). Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Research 39, 4900–4915.CrossRefGoogle Scholar
Beisel, C. L. & Storz, G. (2011). The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Molecular Cell 41, 286–297.CrossRefGoogle Scholar
Bernstein, J. A., Lin, P. H., Cohen, S. N. & Lin-Chao, S. (2004). Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 101, 2758–2763.CrossRefGoogle ScholarPubMed
Blum, E., Py, B., Carpousis, A. J. & Higgins, C. F. (1997). Polyphosphate kinase is a component of the Escherichia coli RNA degradosome. Molecular Microbiology 26, 387–398.CrossRefGoogle ScholarPubMed
Bohn, C., Rigoulay, C., Chabelskaya, S., Sharma, C. M., Marchais, A., Skorski, P., Borezee-Durant, E., Barbet, R., Jacquet, E., Jacq, A., Gautheret, D., Felden, B., Vogel, J. & Bouloc, P. (2010). Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Research 38, 6620–6636.CrossRefGoogle ScholarPubMed
Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E. & Conti, E. (2009). The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139, 547–559.CrossRefGoogle ScholarPubMed
Bouvier, M. & Carpousis, A. J. (2011). A tale of two mRNA degradation pathways mediated by RNase E. Molecular Microbiology. doi:10.1111/j.1365-2958.2011.07894.x.CrossRefGoogle ScholarPubMed
Bouvier, M., Sharma, C. M., Mika, F., Nierhaus, K. H. & Vogel, J. (2008). Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Molecular Cell 32, 827–837.CrossRefGoogle ScholarPubMed
Brandt, F., Etchells, S. A., Ortiz, J. O., Elcock, A. H., Hartl, F. U. & Baumeister, W. (2009). The native 3D organization of bacterial polysomes. Cell 136, 261–271.CrossRefGoogle ScholarPubMed
Brennan, R. G. & Link, T. M. (2007). Hfq structure, function and ligand binding. Current Opinion in Microbiology 10, 125–133.CrossRefGoogle ScholarPubMed
Briant, D. J., Hankins, J. S., Cook, M. A. & Mackie, G. A. (2003). The quaternary structure of RNase G from Escherichia coli. Molecular Microbiology 50, 1381–1390.CrossRefGoogle ScholarPubMed
Britton, R. A., Wen, T., Schaefer, L., Pellegrini, O., Uicker, W. C., Mathy, N., Tobin, C., Daou, R., Szyk, J. & Condon, C. (2007). Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Molecular Microbiology 63, 127–138.CrossRefGoogle ScholarPubMed
Brown, J. W. & Reeve, J. N. (1985). Polyadenylated, noncapped RNA from the archaebacterium Methanococcus vannielii. Journal of Bacteriology 162, 909–917.CrossRefGoogle ScholarPubMed
Butland, G., Peregrin-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J. & Emili, A. (2005). Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537.CrossRefGoogle ScholarPubMed
Callaghan, A. J., Aurikko, J. P., Ilag, L. L., Grossmann, J. G., Chandran, V., Kühnel, K., Poljak, L., Carpousis, A. J., Robinson, C. V., Symmons, M. F. & Luisi, B. F. (2004). Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. Journal of Molecular Biology 340, 965–979.CrossRefGoogle ScholarPubMed
Callaghan, A. J., Grossmann, J. G., Redko, Y. U., Ilag, L. L., Moncrieffe, M. C., Symmons, M. F., Robinson, C. V., Mcdowall, K. J. & Luisi, B. F. (2003). Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain. Biochemistry 42, 13848–13855.CrossRefGoogle ScholarPubMed
Callaghan, A. J., Marcaida, M. J., Stead, J. A., Mcdowall, K. J., Scott, W. G. & Luisi, B. F. (2005a). Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437, 1187–1191.CrossRefGoogle ScholarPubMed
Callaghan, A. J., Redko, Y., Murphy, L. M., Grossmann, J. G., Yates, D., Garman, E., Ilag, L. L., Robinson, C. V., Symmons, M. F., Mcdowall, K. J. & Luisi, B. F. (2005b). “Zn-link”: a metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E. Biochemistry 4667–4675.CrossRefGoogle ScholarPubMed
Callebaut, I., Moshous, D., Mornon, J. P. & De Villartay, J. P. (2002). Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Nucleic Acids Research 30, 3592–3601.CrossRefGoogle ScholarPubMed
Carabetta, V. J., Silhavy, T. J. & Cristea, I. M. (2010). The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. Journal of Bacteriology 192, 3713–3721.CrossRefGoogle Scholar
Carpousis, A. J. (2007). The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annual Review of Microbiology 61, 71–87.CrossRefGoogle ScholarPubMed
Carpousis, A. J., Luisi, B. F. & Mcdowall, K. J. (2009). Endonucleolytic initiation of mRNA decay in Escherichia coli. Progress in Molecular Biology and Translational Science 85, 91–135.CrossRefGoogle ScholarPubMed
Carpousis, A. J., Van Houwe, G., Ehretsmann, C. & Krisch, H. M. (1994). Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76, 889–900.CrossRefGoogle ScholarPubMed
Caruthers, J. M., Feng, Y. N., Mckay, D. B. & Cohen, S. N. (2006). Retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation. Journal of Biological Chemistry 281, 27046–27051.CrossRefGoogle ScholarPubMed
Celesnik, H., Deana, A. & Belasco, J. G. (2007). Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal. Molecular Cell 27, 79–90.CrossRefGoogle ScholarPubMed
Chandran, V. & Luisi, B. F. (2006). Recognition of enolase in the Escherichia coli RNA degradosome. Journal of Molecular Biology 358, 8–15.CrossRefGoogle ScholarPubMed
Chandran, V., Poljak, L., Vanzo, N. F., Leroy, A., Miguel, R. N., Fernandez-Recio, J., Parkinson, J., Burns, C., Carpousis, A. J. & Luisi, B. F. (2007). Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. Journal of Molecular Biology 367, 113–132.CrossRefGoogle ScholarPubMed
Chao, Y. J. & Vogel, J. (2010). The role of Hfq in bacterial pathogens. Current Opinion in Microbiology 13, 24–33.CrossRefGoogle ScholarPubMed
Charollais, J., Dreyfus, M. & Iost, I. (2004). CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Research 32, 2751–2759.CrossRefGoogle ScholarPubMed
Cheng, Z. F. & Deutscher, M. P. (2003). Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proceedings of the National Academy of Sciences of the United States of America 100, 6388–6393.CrossRefGoogle ScholarPubMed
Clouet-D'orval, B., Rinaldi, D., Quentin, Y. & Carpousis, A. J. (2010). Euryarchaeal β-CASP Proteins with homology to bacterial RNase J have 5′ to 3′ exoribonuclease activity. Journal of Biological Chemistry 285, 17574–17583.CrossRefGoogle ScholarPubMed
Coburn, G. A., Miao, X., Briant, D. J. & Mackie, G. A. (1999). Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes and Development 13, 2594–2603.CrossRefGoogle Scholar
Cole, S. E., Lariviere, F. J., Merrikh, C. N. & Moore, M. J. (2009). A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Molecular Cell 34, 440–450.CrossRefGoogle ScholarPubMed
Collins, J. A., Irnov, I., Baker, S. & Winkler, W. C. (2007). Mechanism of mRNA destabilization by the glmS ribozyme. Genes and Development 21, 3356–3368.CrossRefGoogle ScholarPubMed
Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009). Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Molecular and Cellular Proteomics 8, 1350–1360.CrossRefGoogle ScholarPubMed
Condon, C. (2003). RNA processing and degradation in Bacillus subtilis. Microbiology and Molecular Biology Reviews 67, 157–174.CrossRefGoogle ScholarPubMed
Condon, C., Putzer, H., Luo, D. & Grunberg-Manago, M. (1997). Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent in Escherichia coli. Journal of Molecular Biology 268, 235–242.CrossRefGoogle ScholarPubMed
Cordin, O., Banroques, J., Tanner, N. K. & Linder, P. (2006). The DEAD-box protein family of RNA helicases. Gene 367, 17–37.CrossRefGoogle ScholarPubMed
Danchin, A. (1997). Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. DNA Research 4, 9–18.CrossRefGoogle Scholar
Daou-Chabo, R., Mathy, N., Benard, L. & Condon, C. (2009). Ribosomes initiating translation of the hbs mRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1. Molecular Microbiology 71, 1538–1550.CrossRefGoogle ScholarPubMed
Daran-Lapujade, P., Rossell, S., Van Gulik, W. M., Luttik, M. A., De Groot, M. J., Slijper, M., Heck, A. J., Daran, J. M., De Winde, J. H., Westerhoff, H. V., Pronk, J. T. & Bakker, B. M. (2007). The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proceedings of the National Academy of Sciences of the United States of America 104, 15753–15758.CrossRefGoogle ScholarPubMed
De La Sierra-Gallay, I. L., Zig, L., Jamalli, A. & Putzer, H. (2008). Structural insights into the dual activity of RNase J. Nature Structural & Molecular Biology 15, 206–212.CrossRefGoogle Scholar
Deana, A., Celesnik, H. & Belasco, J. G. (2008). The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451, 355–358.CrossRefGoogle ScholarPubMed
Del Favero, M., Mazzantini, E., Briani, F., Zangrossi, S., Tortora, P. & Deho, G. (2008). Regulation of Escherichia coli polynucleotide phosphorylase by ATP. Journal of Biological Chemistry 283, 27355–27359.CrossRefGoogle ScholarPubMed
Depristo, M. A., Weinreich, D. M. & Hartl, D. L. (2005). Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Reviews Genetics 6, 678–687.CrossRefGoogle ScholarPubMed
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J. F., Guindon, S., Lefort, V., Lescot, M., Claverie, J. M. & Gascuel, O. (2008). Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research 36, W465–W469.CrossRefGoogle ScholarPubMed
Deutscher, M. P. (2006). Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Research 34, 659–666.CrossRefGoogle ScholarPubMed
Deutscher, M. P. (2009). Maturation and degradation of ribosomal RNA in bacteria. Progress in Molecular Biology and Translational Science 85, 369–391.CrossRefGoogle ScholarPubMed
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N. P., Trave, G. & Gibson, T. J. (2008). Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers in Bioscience 13, 6580–6603.CrossRefGoogle ScholarPubMed
Dominguez-Escobar, J., Chastanet, A., Crevenna, A. H., Fromion, V., Wedlich-Soldner, R. & Carballido-Lopez, R. (2011). Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 333, 225–228.CrossRefGoogle ScholarPubMed
Dunker, A. K., Silman, I., Uversky, V. N. & Sussman, J. L. (2008). Function and structure of inherently disordered proteins. Current Opinion in Structural Biology 18, 756–764.CrossRefGoogle ScholarPubMed
Dziembowski, A., Piwowarski, J., Hoser, R., Minczuk, M., Dmochowska, A., Siep, M., Van Der Spek, H., Grivell, L. & Stepien, P. P. (2003). The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolism. Journal of Biological Chemistry 278, 1603–1611.CrossRefGoogle ScholarPubMed
Ehretsmann, C. P., Carpousis, A. J. & Krisch, H. M. (1992). Specificity of Escherichia coli endoribonuclease Rnase-E – in vivo and in vitro analysis of mutants in a bacteriophage-T4 messenger-RNA processing site. Genes and Development 6, 149–159.CrossRefGoogle Scholar
Erce, M. A., Low, J. K. K., March, P. E., Wilkins, M. R. & Takayama, K. M. (2009). Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1794, 1107–1114.CrossRefGoogle ScholarPubMed
Erce, M. A., Low, J. K. K. & Wilkins, M. R. (2010). Analysis of the RNA degradosome complex in Vibrio angustum S14. FEBS Journal 277, 5161–5173.CrossRefGoogle ScholarPubMed
Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D. & Putzer, H. (2005). Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Research 33, 2141–2152.CrossRefGoogle Scholar
Evguenieva-Hackenberg, E. & Klug, G. (2009). RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Progress in Molecular Biology and Translational Science 85, 275–317.CrossRefGoogle ScholarPubMed
Fozo, E. M., Hemm, M. R. & Storz, G. (2008). Small toxic proteins and the antisense RNAs that repress them. Microbiology and Molecular Biology Review 72, 579–589.CrossRefGoogle Scholar
Frank, D. N. & Pace, N. R. (1998). Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annual Review of Biochemistry 67, 153–180.CrossRefGoogle Scholar
French, S. L., Santangelo, T. J., Beyer, A. L. & Reeve, J. N. (2007). Transcription and translation are coupled in Archaea. Molecular Biology and Evolution 24, 893–895.CrossRefGoogle ScholarPubMed
Gao, J., Lee, K., Zhao, M., Qiu, J., Zhan, X., Saxena, A., Moore, C. J., Cohen, S. N. & Georgiou, G. (2006). Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Molecular Microbiology 61, 394–406.CrossRefGoogle ScholarPubMed
Garneau, N. L., Wilusz, J. & Wilusz, C. J. (2007). The highways and byways of mRNA decay. Nature Reviews Molecular and Cell Biology 8, 113–126.CrossRefGoogle ScholarPubMed
Garrey, S. M., Blech, M., Riffell, J. L., Hankins, J. S., Stickney, L. M., Diver, M., Hsu, Y. H. R., Kunanithy, V. & Mackie, G. A. (2009). Substrate binding and active site residues in RNases E and G: role of the 5′-sensor. Journal of Biological Chemistry 284, 31843–31850.CrossRefGoogle Scholar
Garrey, S. M. & Mackie, G. A. (2011). Roles of the 5′-phosphate sensor domain in RNase E. Molecular Microbiology 80, 1613–1624.CrossRefGoogle ScholarPubMed
Gatewood, M. L. & Jones, G. H. (2010). (p)ppGpp inhibits polynucleotide phosphorylase from Streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor. Journal of Bacteriology 192, 4275–4280.CrossRefGoogle Scholar
Gibson, T. J. (2009). Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences 34, 471–482.CrossRefGoogle ScholarPubMed
Giorgi, C., Yeo, G. W., Stone, M. E., Katz, D. B., Burge, C., Turrigiano, G. & Moore, M. J. (2007). The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 130, 179–191.CrossRefGoogle ScholarPubMed
Görke, B. & Vogel, J. (2008). Noncoding RNA control of the making and breaking of sugars. Genes and Development 22, 2914–2925.CrossRefGoogle ScholarPubMed
Górna, M. W. (2010). Structural and functional studies of the Escherichia coli RNA degradosome. PhD thesis, University of Cambridge.Google Scholar
Górna, M. W., Pietras, Z., Tsai, Y. C., Callaghan, A. J., Hernandez, H., Robinson, C. V. & Luisi, B. F. (2010). The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 16, 553–562.CrossRefGoogle ScholarPubMed
Gottesman, S. (2005). Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21, 399–404.CrossRefGoogle ScholarPubMed
Gottesman, S. & Storz, G. (2010). Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harbor Perspectives in Biology doi:10.1101/cshperspect.a003798.Google Scholar
Grunberg-Manago, M. (1999). Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annual Review of Genetics 33, 193–227.CrossRefGoogle ScholarPubMed
Gualerzi, C. O., Giuliodori, A. M. & Pon, C. L. (2003). Transcriptional and post-transcriptional control of cold-shock genes. Journal of Molecular Biology 331, 527–539.CrossRefGoogle ScholarPubMed
Gunasekaran, K., Tsai, C. J., Kumar, S., Zanuy, D. & Nussinov, R. (2003). Extended disordered proteins: targeting function with less scaffold. Trends in Biochemical Sciences 28, 81–85.CrossRefGoogle ScholarPubMed
Hardiman, T., Lemuth, K., Keller, M. A., Reuss, M. & Siemann-Herzberg, M. (2007). Topology of the global regulatory network of carbon limitation in Escherichia coli. Journal of Biotechnology 132, 359–374.CrossRefGoogle ScholarPubMed
Hardwick, S. W., Chan, V. S. Y., Broadhurst, R. W. & Luisi, B. F. (2010). An RNA degradosome assembly in Caulobacter crescentus. Nucleic Acids Research 39, 1449–1459.CrossRefGoogle ScholarPubMed
Hasenohrl, D., Lombo, T., Kaberdin, V., Londei, P. & Blasi, U. (2008). Translation initiation factor a/eIF2(-gamma) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus. Proceedings of the National Academy of Sciences of the United States of America 105, 2146–2150.CrossRefGoogle ScholarPubMed
Henkin, T. M. (2008). Riboswitch RNAs: using RNA to sense cellular metabolism. Genes and Development 22, 3383–3390.CrossRefGoogle ScholarPubMed
Houseley, J. & Tollervey, D. (2009). The many pathways of RNA degradation. Cell 136, 763–776.CrossRefGoogle ScholarPubMed
Hu, W., Sweet, T. J., Chamnongpol, S., Baker, K. E. & Coller, J. (2009). Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225–229.CrossRefGoogle ScholarPubMed
Hunt, A., Rawlins, J. P., Thomaides, H. B. & Errington, J. (2006). Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895–2907.CrossRefGoogle ScholarPubMed
Hunter, C. A. & Anderson, H. L. (2009). What is Cooperativity? Angewandte Chemie-International Edition 48, 7488–7499.CrossRefGoogle ScholarPubMed
Ikeda, Y., Yagi, M., Morita, T. & Aiba, H. (2011). Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Molecular Microbiology 79, 419–432.CrossRefGoogle ScholarPubMed
Iost, I. & Dreyfus, M. (2006). DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Research 34, 4189–4197.CrossRefGoogle ScholarPubMed
Jäger, S., Fuhrmann, O., Heck, C., Hebermehl, M., Schiltz, E., Rauhut, R. & Klug, G. (2001). An mRNA degrading complex in Rhodobacter capsulatus. Nucleic Acids Research 29, 4581–4588.CrossRefGoogle ScholarPubMed
Jain, C. (2008). The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly. RNA 14, 381–389.CrossRefGoogle Scholar
Janga, S. C. & Babu, M. M. (2009). Transcript stability in the protein interaction network of Escherichia coli. Molecular BioSystems 5, 154–162.CrossRefGoogle ScholarPubMed
Jankowsky, E. (2011). RNA helicases at work: binding and rearranging. Trends in Biochemical Sciences 36, 19–29.CrossRefGoogle ScholarPubMed
Jiang, X. & Belasco, J. G. (2004). Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA. Proceedings of the National Academy of Sciences of the United States of America 101, 9211–9216.CrossRefGoogle ScholarPubMed
Jourdan, S. S. & Mcdowall, K. J. (2008). Sensing of 5′ monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo. Molecular Microbiology 67, 102–115.CrossRefGoogle ScholarPubMed
Kaberdin, V. R. & Lin-Chao, S. (2009). Unraveling new roles for minor components of the E. coli RNA degradosome. RNA Biology 6, 402–405.CrossRefGoogle ScholarPubMed
Kaberdin, V. R., Walsh, A. P., Jakobsen, T., Mcdowall, K. J. & Von Gabain, A. (2000). Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E. Journal of Molecular Biology 301, 257–264.CrossRefGoogle ScholarPubMed
Kanai, A., Oida, H., Matsuura, N. & Doi, H. (2003). Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochemical Journal 372, 253–261.CrossRefGoogle ScholarPubMed
Kang, S. O., Caparon, M. G. & Cho, K. H. (2010). Virulence gene regulation by CvfA, a putative RNase: the CvfA–enolase complex in Streptococcus pyogenes links nutritional stress, growth-phase control, and virulence gene expression. Infection and Immunity 78, 2754–2767.CrossRefGoogle ScholarPubMed
Kato, J. I. & Hashimoto, M. (2007). Construction of consecutive deletions of the Escherichia coli chromosome. Molecular Systems Biology 3, 132.CrossRefGoogle ScholarPubMed
Khemici, V. & Carpousis, A. J. (2004). The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Molecular Microbiology 51, 777–790.CrossRefGoogle ScholarPubMed
Khemici, V., Poljak, L., Luisi, B. F. & Carpousis, A. J. (2008). The RNase E of Escherichia coli is a membrane-binding protein. Molecular Microbiology 70, 799–813.CrossRefGoogle ScholarPubMed
Khemici, V., Poljak, L., Toesca, I. & Carpousis, A. J. (2005). Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proceedings of the National Academy of Sciences of the United States of America 102, 6913–6918.CrossRefGoogle ScholarPubMed
Khemici, V., Toesca, I., Poljak, L., Vanzo, N. F. & Carpousis, A. J. (2004). The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE. Molecular Microbiology 54, 1422–1430.CrossRefGoogle Scholar
Kido, M., Yamanaka, K., Mitani, T., Niki, H., Ogura, T. & Hiraga, S. (1996). RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. Journal of Bacteriology 178, 3917–3925.CrossRefGoogle ScholarPubMed
Kim, K. S. & Lee, Y. (2004). Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Research 32, 6057–6068.CrossRefGoogle ScholarPubMed
Kime, L., Jourdan, S. S., Stead, J. A., Hidalgo-Sastre, A. & Mcdowall, K. J. (2010). Rapid cleavage of RNA by RNase E in the absence of 5′ monophosphate stimulation. Molecular Microbiology 76, 590–604.CrossRefGoogle ScholarPubMed
Koonin, E. V., Wolf, Y. I. & Aravind, L. (2001). Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Research 11, 240–252.CrossRefGoogle ScholarPubMed
Koslover, D. J., Callaghan, A. J., Marcaida, M. J., Garman, E. F., Martick, M., Scott, W. G. & Luisi, B. F. (2008). The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure 16, 1238–1244.CrossRefGoogle Scholar
Kovacs, L., Csanadi, A., Megyeri, K., Kaberdin, V. R. & Miczak, A. (2005). Mycobacterial RNase E-associated proteins. Microbiology and Immunology 49, 1003–1007.CrossRefGoogle ScholarPubMed
Lebreton, A., Tomecki, R., Dziembowski, A. & Seraphin, B. (2008). Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456, 993–996.CrossRefGoogle ScholarPubMed
Lee, K., Bernstein, J. A. & Cohen, S. N. (2002). RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Molecular Microbiology 43, 1445–1456.CrossRefGoogle ScholarPubMed
Lee, K. & Cohen, S. N. (2003). A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Molecular Microbiology 48, 349–360.CrossRefGoogle ScholarPubMed
Lee, K., Zhan, X., Gao, J., Qiu, J., Feng, Y., Meganathan, R., Cohen, S. N. & Georgiou, G. (2003). RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114, 623–634.Google ScholarPubMed
Lehnik-Habrink, M., Pfortner, H., Rempeters, L., Pietack, N., Herzberg, C. & Stulke, J. (2010). The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Molecular Microbiology 77, 958–971.CrossRefGoogle ScholarPubMed
Lehnik-Habrink, M., Newman, J., Rothe, F. M., Solovyova, A. S., Rodrigues, C., Herzberg, C., Commichau, F. M., Lewis, R. J. & Stulke, J. (2011). RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent to RNase E from Escherichia coli. Journal of Bacteriology 193, 5431–5441.CrossRefGoogle ScholarPubMed
Leibundgut, M., Maier, T., Jenni, S. & Ban, N. (2008). The multienzyme architecture of eukaryotic fatty acid synthases. Current Opinion in Structural Biology 18, 714–725.CrossRefGoogle ScholarPubMed
Leroy, A., Vanzo, N. F., Sousa, S., Dreyfus, M. & Carpousis, A. J. (2002). Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Molecular Microbiology 45, 1231–1243.CrossRefGoogle ScholarPubMed
Li, Z. & Deutscher, M. P. (2002). RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8, 97–109.CrossRefGoogle ScholarPubMed
Lin-Chao, S., Wei, C. L. & Lin, Y. T. (1999). RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity. Proceedings of the National Academy of Sciences of the United States of America 96, 12406–12411.CrossRefGoogle ScholarPubMed
Lin-Chao, S., Wong, T. T., Mcdowall, K. J. & Cohen, S. N. (1994). Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. Journal of Biological Chemistry 269, 10797–10803.CrossRefGoogle ScholarPubMed
Link, T. M., Valentin-Hansen, P. & Brennan, R. G. (2009). Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proceedings of the National Academy of Sciences of the United States of America 106, 19286–19291.Google ScholarPubMed
Liou, G. G., Chang, H. Y., Lin, C. S. & Lin-Chao, S. (2002). DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E. Journal of Biological Chemistry 277, 41157–41162.CrossRefGoogle ScholarPubMed
Liou, G. G., Jane, W. N., Cohen, S. N., Lin, N. S. & Lin-Chao, S. (2001). RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E. Proceedings of the National Academy of Sciences of the United States of America 98, 63–68.CrossRefGoogle ScholarPubMed
Lobley, A., Swindells, M. B., Orengo, C. A. & Jones, D. T. (2007). Inferring function using patterns of native disorder in proteins. PLoS Computational Biology 3, 1567–1579.CrossRefGoogle ScholarPubMed
Lopez, P. J., Marchand, I., Joyce, S. A. & Dreyfus, M. (1999). The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Molecular Microbiology 33, 188–199.CrossRefGoogle Scholar
Lorentzen, E., Walter, P., Fribourg, S., Evguenieva-Hackenberg, E., Klug, G. & Conti, E. (2005). The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Structural and Molecular Biology 12, 575–581.CrossRefGoogle ScholarPubMed
Lundberg, U. & Altman, S. (1995). Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA 1, 327–334.Google Scholar
Lykke-Andersen, S., Brodersen, D. E. & Jensen, T. H. (2009). Origins and activities of the eukaryotic exosome. Journal of Cell Science 122, 1487–1494.CrossRefGoogle ScholarPubMed
Mackie, G. A. (1998). Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395, 720–723.CrossRefGoogle ScholarPubMed
Mackie, G. A. (2000). Stabilization of circular rpsT mRNA demonstrates the 5′-end dependence of RNase E action in vivo. Journal of Biological Chemistry 275, 25069–25072.CrossRefGoogle ScholarPubMed
Majdalani, N., Vanderpool, C. K. & Gottesman, S. (2005). Bacterial small RNA regulators. Critical Reviews in Biochemistry and Molecular Biology 40, 93–113.CrossRefGoogle ScholarPubMed
Malecki, M., Jedrzejczak, R., Stepien, P. P. & Golik, P. (2007). In vitro reconstitution and characterization of the yeast mitochondrial degradosome complex unravels tight functional interdependence. Journal of Molecular Biology 372, 23–36.CrossRefGoogle ScholarPubMed
Marcaida, M. J., Depristo, M. A., Chandran, V., Carpousis, A. J. & Luisi, B. F. (2006). The RNA degradosome: life in the fast lane of adaptive molecular evolution. Trends in Biochemical Sciences 31, 359–365.CrossRefGoogle Scholar
Massé, E., Escorcia, F. E. & Gottesman, S. (2003). Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes and Development 17, 2374–2383.CrossRefGoogle ScholarPubMed
Massé, E., Salvail, H., Desnoyers, G. & Arguin, M. (2007). Small RNAs controlling iron metabolism. Current Opinion in Microbiology 10, 140–145.CrossRefGoogle ScholarPubMed
Mathy, N., Benard, L., Pellegrini, O., Daou, R., Wen, T. & Condon, C. (2007). 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129, 681–692.CrossRefGoogle ScholarPubMed
Mcdowall, K. J. & Cohen, S. N. (1996). The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site. Journal of Molecular Biology 255, 349–355.CrossRefGoogle ScholarPubMed
Mcdowall, K. J., Kaberdin, V. R., Wu, S. W., Cohen, S. N. & Lin-Chao, S. (1995). Site-specific RNase E cleavage of oligonucleotides and inhibition by stem-loops. Nature 374, 287–290.CrossRefGoogle ScholarPubMed
Mcdowall, K. J., Lin-Chao, S. & Cohen, S. N. (1994). A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. Journal of Biological Chemistry 269, 10790–10796.CrossRefGoogle ScholarPubMed
Miczak, A., Kaberdin, V. R., Wei, C. L. & Lin-Chao, S. (1996). Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proceedings of the National Academy of Sciences of the United States of America 93, 3865–3869.CrossRefGoogle Scholar
Miczak, A., Srivastava, R. A. & Apirion, D. (1991). Location of the RNA-processing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell. Molecular Microbiology 5, 1801–1810.CrossRefGoogle ScholarPubMed
Milner-White, E. J., Pietras, Z. & Luisi, B. F. (2010). An ancient anion-binding structural module in RNA and DNA helicases. Proteins 78, 1900–1908.CrossRefGoogle ScholarPubMed
Mohanty, B. K. & Kushner, S. R. (2000). Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Molecular Microbiology 36, 982–994.CrossRefGoogle ScholarPubMed
Montero Llopis, P., Jackson, A. F., Sliusarenko, O., Surovtsev, I., Heinritz, J., Emonet, T. & Jacobs-Wagner, C. (2010). Spatial organization of the flow of genetic information in bacteria. Nature 466, 77–81.CrossRefGoogle ScholarPubMed
Morita, T., Kawamoto, H., Mizota, T., Inada, T. & Aiba, H. (2004). Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Molecular Microbiology 54, 1063–1075.CrossRefGoogle Scholar
Morita, T., Maki, K. & Aiba, H. (2005). RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes and Development 19, 2176–2186.CrossRefGoogle ScholarPubMed
Mudd, E. A., Sullivan, S., Gisby, M. F., Mironov, A., Kwon, C. S., Chung, W. I. & Day, A. (2008). A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis. Journal of Experimental Botany 59, 2597–2610.CrossRefGoogle ScholarPubMed
Nevo-Dinur, K., Nussbaum-Shochat, A., Ben-Yehuda, S. & Amster-Choder, O. (2011). Translation-independent localization of mRNA in E. coli. Science 331, 1081–1084.CrossRefGoogle ScholarPubMed
Newbury, S. F., Smith, N. H. & Higgins, C. F. (1987a). Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51, 1131–1143.CrossRefGoogle ScholarPubMed
Newbury, S. F., Smith, N. H., Robinson, E. C., Hiles, I. D. & Higgins, C. F. (1987b). Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48, 297–310.CrossRefGoogle ScholarPubMed
Nurmohamed, S., Mckay, A. R., Robinson, C. V. & Luisi, B. F. (2010). Molecular recognition between Escherichia coli enolase and ribonuclease E. Acta crystallographica. Section D, Biological Crystallography 66, 1036–1040.CrossRefGoogle Scholar
Nurmohamed, S., Vaidialingam, B., Callaghan, A. J. & Luisi, B. F. (2009). Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Journal of Molecular Biology 389, 17–33.CrossRefGoogle ScholarPubMed
Nurmohamed, S., Vincent, H. A., Titman, C. M., Chandran, V., Pears, M. R., Du, D., Griffin, J. L., Callaghan, A. J. & Luisi, B. F. (2011). Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. Journal of Biological Chemistry 286, 14315–14323.CrossRefGoogle ScholarPubMed
Opdyke, J. A., Kang, J. G. & Storz, G. (2004). GadY, a small-RNA regulator of acid response genes in Escherichia coli. Journal of Bacteriology 186, 6698–6705.CrossRefGoogle Scholar
Ow, M. C. & Kushner, S. R. (2002). Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes and Development 16, 1102–1115.CrossRefGoogle ScholarPubMed
Ow, M. C., Liu, Q. & Kushner, S. R. (2000). Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Molecular Microbiology 38, 854–866.CrossRefGoogle ScholarPubMed
Papenfort, K., Said, N., Welsink, T., Lucchini, S., Hinton, J. C. D. & Vogel, J. (2009). Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Molecular Microbiology 74, 139–158.CrossRefGoogle ScholarPubMed
Pechmann, S., Levy, E. D., Tartaglia, G. G. & Vendruscolo, M. (2009). Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins. Proceedings of the National Academy of Sciences of the United States of America 106, 10159–10164.CrossRefGoogle ScholarPubMed
Peil, L., Virumae, K. & Remme, J. (2008). Ribosome assembly in Escherichia coli strains lacking the RNA helicase DeaD/CsdA or DbpA. The FEBS Journal 275, 3772–3782.CrossRefGoogle ScholarPubMed
Pfeiffer, V., Papenfort, K., Lucchini, S., Hinton, J. C. D. & Vogel, J. (2009). Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nature Structural and Molecular Biology 16, 840–843.CrossRefGoogle ScholarPubMed
Pichon, C. & Felden, B. (2007). Proteins that interact with bacterial small RNA regulators. FEMS Microbiology Reviews 31, 614–625.CrossRefGoogle ScholarPubMed
Portnoy, V. & Schuster, G. (2006). RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Research 34, 5923–5931.CrossRefGoogle ScholarPubMed
Prévost, K., Salvail, H., Desnoyers, G., Jacques, J. F., Phaneuf, E. & Massé, E. (2007). The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Molecular Microbiology 64, 1260–1273.CrossRefGoogle ScholarPubMed
Prud'Homme-généreux, A., Beran, R. K., Iost, I., Ramey, C. S., Mackie, G. A. & Simons, R. W. (2004). Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a ‘cold shock degradosome’. Molecular Microbiology 54, 1409–1421.CrossRefGoogle ScholarPubMed
Purusharth, R. I., Klein, F., Sulthana, S., Jäger, S., Jagannadham, M. V., Evguenieva-Hackenberg, E., Ray, M. K. & Klug, G. (2005). Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W. Journal of Biological Chemistry 280, 14572–14578.CrossRefGoogle Scholar
Py, B., Causton, H., Mudd, E. A. & Higgins, C. F. (1994). A protein complex mediating mRNA degradation in Escherichia coli. Molecular Microbiology 14, 717–729.CrossRefGoogle ScholarPubMed
Py, B., Higgins, C. F., Krisch, H. M. & Carpousis, A. J. (1996). A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169–172.CrossRefGoogle ScholarPubMed
Pyle, A. M. (2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annual Review of Biophysics 37, 317–336.CrossRefGoogle ScholarPubMed
Radford, H. E., Meijer, H. A. & De Moor, C. H. (2008). Translational control by cytoplasmic polyadenylation in Xenopus oocytes. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1779, 217–229.CrossRefGoogle ScholarPubMed
Redko, Y., Li De Lasierra-Gallay, I. & Condon, C. (2007). When all's zed and done: the structure and function of RNase Z in prokaryotes. Nature Reviews Microbiology 5, 278–286.CrossRefGoogle ScholarPubMed
Remaut, H. & Waksman, G. (2006). Protein–protein interaction through beta-strand addition. Trends in Biochemical Sciences 31, 436–444.CrossRefGoogle ScholarPubMed
Rissland, O. S. & Norbury, C. J. (2009). Decapping is preceded by 3′ uridylation in a novel pathway of bulk mRNA turnover. Nature Structural and Molecular Biology 16, 616–U656.CrossRefGoogle Scholar
Roth, A. & Breaker, R. R. (2009). The structural and functional diversity of metabolite-binding riboswitches. Annual Review of Biochemistry 78, 305–334.CrossRefGoogle ScholarPubMed
Roux, C. M., Demuth, J. P. & Dunman, P. M. (2011). Characterization of components of the Staphylococcus aureus messenger RNA degradosome holoenzyme-like complex. Journal of Bacteriology 193, 5520–5526.CrossRefGoogle ScholarPubMed
Russell, R. B. & Gibson, T. J. (2008). A careful disorderliness in the proteome: sites for interaction and targets for future therapies. FEBS Letters 582, 1271–1275.CrossRefGoogle ScholarPubMed
Sabnis, N. A., Yang, H. H. & Romeo, T. (1995). Pleiotropic regulation of central carbohydrate-metabolism in Escherichia coli via the gene csrA. Journal of Biological Chemistry 270, 29096–29104.CrossRefGoogle ScholarPubMed
Sauer, E. & Weichenrieder, O. (2011). Structural basis for RNA 3′-end recognition by Hfq. Proceedings of the National Academy of Sciences of the United States of America 108, 13065–13070.CrossRefGoogle ScholarPubMed
Schaeffer, D., Tsanova, B., Barbas, A., Reis, F. P., Dastidar, E. G., Sanchez-Rotunno, M., Arraiano, C. M. & Van Hoof, A. (2009). The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nature Structural and Molecular Biology 16, 56–62.CrossRefGoogle ScholarPubMed
Schein, A., Sheffy-Levin, S., Glaser, F. & Schuster, G. (2008). The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme. RNA 14, 1057–1068.CrossRefGoogle Scholar
Schiffer, S., Rosch, S. & Marchfelder, A. (2002). Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes. EMBO Journal 21, 2769–2777.CrossRefGoogle ScholarPubMed
Schubert, M., Edge, R. E., Lario, P., Cook, M. A., Strynadka, N. C., Mackie, G. A. & Mcintosh, L. P. (2004). Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces. Journal of Molecular Biology 341, 37–54.CrossRefGoogle ScholarPubMed
Schuck, A., Diwa, A. & Belasco, J. G. (2009). RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5′ untranslated region. Molecular Microbiology 72, 470–478.CrossRefGoogle ScholarPubMed
Schumacher, M. A., Pearson, R. F., Moller, T., Valentin-Hansen, P. & Brennan, R. G. (2002). Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO Journal 21, 3546–3556.CrossRefGoogle Scholar
Shahbabian, K., Jamalli, A., Zig, L. & Putzer, H. (2009). RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO Journal 28, 2523–2533.CrossRefGoogle Scholar
Sharpe Elles, L. M., Sykes, M. T., Williamson, J. R. & Uhlenbeck, O. C. (2009). A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Research 37, 6503–6514.CrossRefGoogle Scholar
Shevtsov, M. B., Chen, Y. L., Gollnick, P. & Antson, A. A. (2005). Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction. Proceedings of the National Academy of Sciences of the United States of America 102, 17600–17605.CrossRefGoogle ScholarPubMed
Shi, Z., Yang, W. Z., Lin-Chao, S., Chak, K. F. & Yuan, H. S. (2008). Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA 14, 2361–2371.CrossRefGoogle ScholarPubMed
Siculella, L., Damiano, F., Di Summa, R., Tredici, S. M., Alduina, R., Gnoni, G. V. & Alifano, P. (2010). Guanosine 5′-diphosphate 3′-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a ‘rare’ actinomycete. Molecular Microbiology 77, 716–729.CrossRefGoogle Scholar
Singh, D., Chang, S. J., Lin, P. H., Averina, O. V., Kaberdin, V. R. & Lin-Chao, S. (2009). Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 106, 864–869.CrossRefGoogle ScholarPubMed
Sittka, A., Lucchini, S., Papenfort, K., Sharma, C. M., Rolle, K., Binnewies, T. T., Hinton, J. C. D. & Vogel, J. (2008). Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. Plos Genetics 4, e1000163.CrossRefGoogle ScholarPubMed
Stead, M. B., Marshburn, S., Mohanty, B. K., Mitra, J., Castillo, L. P., Ray, D., Van Bakel, H., Hughes, T. R. & Kushner, S. R. (2010). Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Research 39, 3188–3203.CrossRefGoogle ScholarPubMed
Suzuki, K., Babitzke, P., Kushner, S. R. & Romeo, T. (2006). Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes and Development 20, 2605–2617.CrossRefGoogle ScholarPubMed
Symmons, M. F., Jones, G. H. & Luisi, B. F. (2000). A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 8, 1215–1226.CrossRefGoogle ScholarPubMed
Symmons, M. F., Williams, M. G., Luisi, B. F., Jones, G. H. & Carpousis, A. J. (2002). Running rings around RNA: a superfamily of phosphate-dependent RNases. Trends in Biochemical Sciences 27, 11–18.CrossRefGoogle ScholarPubMed
Szczesny, R. J., Borowski, L. S., Brzezniak, L. K., Dmochowska, A., Gewartowski, K., Bartnik, E. & Stepien, P. P. (2009). Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance. Nucleic Acids Research 38, 279–298.CrossRefGoogle ScholarPubMed
Taghbalout, A. & Rothfield, L. (2007). RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proceedings of the National Academy of Sciences of the United States of America 104, 1667–1672.CrossRefGoogle ScholarPubMed
Taghbalout, A. & Rothfield, L. (2008). RNaseE and RNA helicase B play central roles in the cytoskeletal organization of the RNA degradosome. Journal of Biological Chemistry 283, 13850–13855.CrossRefGoogle ScholarPubMed
Taghbalout, A. & Yang, Q. F. (2010). Self-assembly of the bacterial cytoskeleton-associated RNA Helicase B protein into polymeric filamentous structures. Journal of Bacteriology 192, 3222–3226.CrossRefGoogle ScholarPubMed
Takada, A., Nagai, K. & Wachi, M. (2005). A decreased level of FtsZ is responsible for inviability of RNase E-deficient cells. Genes Cells 10, 733–741.CrossRefGoogle ScholarPubMed
Tang, T. H., Rozhdestvensky, T. S., D'Orval, B. C., Bortolin, M. L., Huber, H., Charpentier, B., Branlant, C., Bachellerie, J. P., Brosius, J. & Huttenhofer, A. (2002). RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Research 30, 921–930.CrossRefGoogle ScholarPubMed
Tokuriki, N. & Tawfik, D. S. (2009). Stability effects of mutations and protein evolvability. Current Opinion in Structural Biology 19, 596–604.CrossRefGoogle ScholarPubMed
Toledo-Arana, A., Repoila, F. & Cossart, P. (2007). Small noncoding RNAs controlling pathogenesis. Current Opinion in Microbiology 10, 182–188.CrossRefGoogle ScholarPubMed
Trubetskoy, D., Proux, F., Allemand, F., Dreyfus, M. & Iost, I. (2009). SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo. Nucleic Acids Research 37, 6540–6549.CrossRefGoogle ScholarPubMed
Tu, K. C. & Bassler, B. L. (2007). Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes and Development 21, 221–233.CrossRefGoogle ScholarPubMed
Tuckerman, J. R., Gonzalez, G. & Gilles-Gonzalez, M. A. (2011). Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing. Journal of Molecular Biology 407, 633–639.CrossRefGoogle ScholarPubMed
Valentin-Hansen, P., Johansen, J. & Rasmussen, A. A. (2007). Small RNAs controlling outer membrane porins. Current Opinion in Microbiology 10, 152–155.CrossRefGoogle ScholarPubMed
Vanzo, N. F., Li, Y. S., Py, B., Blum, E., Higgins, C. F., Raynal, L. C., Krisch, H. M. & Carpousis, A. J. (1998). Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes and Development 12, 2770–2781.CrossRefGoogle ScholarPubMed
Vecerek, B., Rajkowitsch, L., Sonnleitner, E., Schroeder, R. & Blasi, U. (2008). The C-terminal domain of Escherichia coli Hfq is required for regulation. Nucleic Acids Research 36, 133–143.CrossRefGoogle ScholarPubMed
Viegas, S. C., Pfeiffer, V., Sittka, A., Silva, I. J., Vogel, J. & Arraiano, C. M. (2007). Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Research 35, 7651–7664.CrossRefGoogle ScholarPubMed
Vogel, J. (2009). A rough guide to the non-coding RNA world of Salmonella. Molecular Microbiology 71, 1–11.CrossRefGoogle Scholar
Vogel, J., Argaman, L., Wagner, E. G. & Altuvia, S. (2004). The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Current Biology 14, 2271–2276.CrossRefGoogle ScholarPubMed
Vogel, J. & Luisi, B. F. (2011). Hfq and its constellation of RNA. Nature Reviews in Microbiology 9, 578–589.CrossRefGoogle ScholarPubMed
Vogel, J. & Papenfort, K. (2006). Small non-coding RNAs and the bacterial outer membrane. Current Opinion in Microbiology 9, 605–611.CrossRefGoogle ScholarPubMed
Wang, D. D., Shu, Z., Lieser, S. A., Chen, P. L. & Lee, W. H. (2009). Human mitochondrial SUV3 and PNPase form a 330 kDa heteropentamer to cooperatively degrade dsRNA with a 3′ to 5′ directionality. Journal of Biological Chemistry 284, 20812–20821.CrossRefGoogle Scholar
Wang, G., Chen, H. W., Oktay, Y., Zhang, J., Allen, E. L., Smith, G. M., Fan, K. C., Hong, J. S., French, S. W., Mccaffery, J. M., Lightowlers, R. N., Morse, H. C., Koehler, C. M. & Teitell, M. A. (2010). PNPase regulates RNA import into mitochondria. Cell 142, 456–467.CrossRefGoogle ScholarPubMed
Wassarman, K. M. (2007). 6S RNA: a small RNA regulator of transcription. Current Opinion in Microbiology 10, 164–168.CrossRefGoogle ScholarPubMed
Waters, L. S. & Storz, G. (2009). Regulatory RNAs in Bacteria. Cell 136, 615–628.CrossRefGoogle ScholarPubMed
Whitty, A. (2008). Cooperativity and biological complexity. Nature Chemical Biology 4, 435–439.CrossRefGoogle ScholarPubMed
Wilusz, C. J. & Wilusz, J. (2004). Bringing the role of rnRNA decay in the control of gene expression into focus. Trends in Genetics 20, 491–497.CrossRefGoogle Scholar
Worrall, J. A., Górna, M., Crump, N. T., Phillips, L. G., Tuck, A. C., Price, A. J., Bavro, V. N. & Luisi, B. F. (2008a). Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. Journal of Molecular Biology 382, 870–883.CrossRefGoogle ScholarPubMed
Worrall, J. A., Howe, F. S., Mckay, A. R., Robinson, C. V. & Luisi, B. F. (2008b). Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase. Journal of Biological Chemistry 283, 5567–5576.CrossRefGoogle ScholarPubMed
Wright, P. E. & Dyson, H. J. (2009). Linking folding and binding. Current Opinion in Structural Biology 19, 31–38.CrossRefGoogle ScholarPubMed
Xiang, S., Cooper-Morgan, A., Jiao, X., Kiledjian, M., Manley, J. L. & Tong, L. (2009). Structure and function of the 5′–>3′ exoribonuclease Rat1 and its activating partner Rai1. Nature 458, 784–788.CrossRefGoogle ScholarPubMed
Xu, F., Lin-Chao, S. & Cohen, S. N. (1993). The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proceedings of the National Academy of Sciences of the United States of America 90, 6756–6760.CrossRefGoogle ScholarPubMed
Yang, J., Jain, C. & Schesser, K. (2008). RNase E regulates the Yersinia type 3 secretion system. Journal of Bacteriology 190, 3774–3778.CrossRefGoogle ScholarPubMed
Yang, W., Lee, J. Y. & Nowotny, M. (2006). Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Molecular Cell 22, 5–13.CrossRefGoogle ScholarPubMed
Yao, S. Y. & Bechhofer, D. H. (2010). Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. Journal of Bacteriology 192, 3279–3286.CrossRefGoogle ScholarPubMed
Zeller, M. E., Csanadi, A., Miczak, A., Rose, T., Bizebard, T. & Kaberdin, V. R. (2007). Quaternary structure and biochemical properties of mycobacterial RNase E/G. Biochemical Journal 403, 207–215.CrossRefGoogle ScholarPubMed
Zhang, J. & Olsen, G. J. (2009). Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii. RNA 15, 1909–1916.CrossRefGoogle ScholarPubMed
Zundel, M. A., Basturea, G. N. & Deutscher, M. P. (2009). Initiation of ribosome degradation during starvation in Escherichia coli. RNA 15, 977–983.CrossRefGoogle ScholarPubMed